4HN1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF H60N/Y130F DOUBLE MUTANT OF CHMJ, A 3'-MONOEPIMERASE FROM STREPTOMYCES BIKINIENSIS IN COMPLEX WITH DTDP

Authors :   H. M. Holden, R. L. Kubiak

Date :   18 Oct 12 (Deposition) - 21 Nov 12 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   3'-Monoepimerase, Natural Product, Deoxysugar, Chalcomycin, Dtdp- Mycinose, Cupin Fold, Nucleotide-Linked Sugar, Epimerization, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. L. Kubiak, R. K. Phillips, M. W. Zmudka, M. R. Ahn, E. M. Maka, G. L. Pyeatt, S. J. Roggensack, H. M. Holden
Structural And Functional Studies On A 3'-Epimerase Involve In The Biosynthesis Of Dtdp-6-Deoxy-D-Allose.
Biochemistry V. 51 9375 2012
PubMed-ID: 23116432 | Reference-DOI: 10.1021/BI3012737

Molecule 1 - PUTATIVE 3-EPIMERASE IN D-ALLOSE PATHWAY
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-31B(+)
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CHMJ
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES BIKINIENSIS
	Organism Taxid	:	1896

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
2	TDR	2	Ligand/Ion	THYMINE
3	THM	2	Ligand/Ion	THYMIDINE
4	TYD	4	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 1 (3, 11)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	TDR	-1	Ligand/Ion	THYMINE
3	THM	2	Ligand/Ion	THYMIDINE
4	TYD	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	TDR	2	Ligand/Ion	THYMINE
3	THM	-1	Ligand/Ion	THYMIDINE
4	TYD	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:62 , TYR A:136 , ALA A:137 , PRO A:138 , HOH A:473	BINDING SITE FOR RESIDUE EDO A 301
02	AC2	SOFTWARE	HIS A:17 , ASP A:19 , ARG A:21 , GLY A:22 , ARG A:23 , SER A:24 , ARG B:57 , TYD B:304	BINDING SITE FOR RESIDUE EDO A 302
03	AC3	SOFTWARE	GLN A:12 , PHE A:28 , ARG A:29 , SER A:32 , TYR A:71 , HOH A:401	BINDING SITE FOR RESIDUE EDO A 303
04	AC4	SOFTWARE	MET A:1 , TRP A:10 , ALA A:36 , HOH A:518 , ASN D:169	BINDING SITE FOR RESIDUE EDO A 304
05	AC5	SOFTWARE	GLN A:45 , ARG A:57 , TYR A:136 , HOH A:450 , HOH A:486 , HOH A:487 , HOH A:509 , HIS B:17 , ARG B:21 , GLU B:26 , EDO B:301 , HOH B:512 , VAL D:15	BINDING SITE FOR RESIDUE TYD A 305
06	AC6	SOFTWARE	ARG A:95 , TRP A:96 , HOH A:415 , HOH A:525	BINDING SITE FOR RESIDUE THM A 306
07	AC7	SOFTWARE	ARG A:57 , TYD A:305 , HIS B:17 , ASP B:19 , ARG B:21 , GLY B:22 , SER B:24	BINDING SITE FOR RESIDUE EDO B 301
08	AC8	SOFTWARE	GLN B:12 , PHE B:28 , ARG B:29 , SER B:32 , TYR B:71 , HOH B:414	BINDING SITE FOR RESIDUE EDO B 302
09	AC9	SOFTWARE	THR B:62 , GLN B:68 , TYR B:136 , ALA B:137 , PRO B:138 , HOH B:467	BINDING SITE FOR RESIDUE EDO B 303
10	BC1	SOFTWARE	HIS A:17 , ARG A:21 , GLU A:26 , EDO A:302 , HOH A:503 , GLN B:45 , ARG B:57 , TYR B:136 , ARG B:166 , HOH B:448 , HOH B:493 , HOH B:506 , VAL C:15	BINDING SITE FOR RESIDUE TYD B 304
11	BC2	SOFTWARE	ARG B:95 , TRP B:96 , HOH B:423 , HOH B:487	BINDING SITE FOR RESIDUE THM B 305
12	BC3	SOFTWARE	HIS C:17 , ASP C:19 , GLY C:22 , SER C:24 , TYD C:303 , ARG D:57	BINDING SITE FOR RESIDUE EDO C 301
13	BC4	SOFTWARE	GLN C:12 , PHE C:28 , ARG C:29 , PHE C:33 , TYR C:71	BINDING SITE FOR RESIDUE EDO C 302
14	BC5	SOFTWARE	VAL A:15 , HIS A:17 , HIS C:17 , ARG C:21 , GLU C:26 , EDO C:301 , HOH C:424 , HOH C:428 , GLN D:45 , ARG D:57 , TYR D:136 , ARG D:166 , HOH D:428	BINDING SITE FOR RESIDUE TYD C 303
15	BC6	SOFTWARE	VAL B:15 , HIS B:17 , GLN C:45 , ARG C:57 , TYR C:136 , ARG C:166 , HOH C:438 , HOH C:441 , HOH C:442 , HIS D:17 , ARG D:21 , GLU D:26 , EDO D:302	BINDING SITE FOR RESIDUE TYD C 304
16	BC7	SOFTWARE	ARG C:95 , TRP C:96 , HOH C:475	BINDING SITE FOR RESIDUE TDR C 305
17	BC8	SOFTWARE	GLN D:12 , PHE D:28 , ARG D:29 , SER D:32 , PHE D:33 , TYR D:71	BINDING SITE FOR RESIDUE EDO D 301
18	BC9	SOFTWARE	ARG C:57 , TYD C:304 , HIS D:17 , ASP D:19 , ARG D:21 , GLY D:22 , SER D:24	BINDING SITE FOR RESIDUE EDO D 302
19	CC1	SOFTWARE	ARG D:95 , TRP D:96 , HOH D:437	BINDING SITE FOR RESIDUE TDR D 303

(no "SS Bond" information available for 4HN1)

Asymmetric Unit

No.	Residues
1	Gly A:58	-	Ile A:59
2	Ile A:64	-	Pro A:65
3	Pro A:65	-	Pro A:66
4	Gly B:58	-	Ile B:59
5	Ile B:64	-	Pro B:65
6	Pro B:65	-	Pro B:66
7	Gly C:58	-	Ile C:59
8	Ile C:64	-	Pro C:65
9	Pro C:65	-	Pro C:66
10	Gly D:58	-	Ile D:59
11	Ile D:64	-	Pro D:65
12	Pro D:65	-	Pro D:66

(no "SAP(SNP)/Variant" information available for 4HN1)

(no "PROSITE Motif" information available for 4HN1)

(no "Exon" information available for 4HN1)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d4hn1a_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee...eeee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hn1 A   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGINYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVFLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEH 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d4hn1b_ B: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee....eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hn1 B   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGINYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVFLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEH 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains d4hn1c_ C: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee...eeee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hn1 C   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGINYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVFLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEHHH 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains d4hn1d_ D: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee....eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hn1 D   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGINYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVFLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEHH 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: RmlC-like cupins (220)

Family: automated matches (27)

Protein domain: automated matches (27)

Streptomyces bikiniensis [TaxId: 1896] (3)

1a	d4hn1a_	A:
1b	d4hn1b_	B:
1c	d4hn1c_	C:
1d	d4hn1d_	D:

(no "CATH Domain" information available for 4HN1)

(no "Pfam Domain" information available for 4HN1)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:58 - Ile A:59	[ RasMol ]
		Gly B:58 - Ile B:59	[ RasMol ]
		Gly C:58 - Ile C:59	[ RasMol ]
		Gly D:58 - Ile D:59	[ RasMol ]
		Ile A:64 - Pro A:65	[ RasMol ]
		Ile B:64 - Pro B:65	[ RasMol ]
		Ile C:64 - Pro C:65	[ RasMol ]
		Ile D:64 - Pro D:65	[ RasMol ]
		Pro A:65 - Pro A:66	[ RasMol ]
		Pro B:65 - Pro B:66	[ RasMol ]
		Pro C:65 - Pro C:66	[ RasMol ]
		Pro D:65 - Pro D:66	[ RasMol ]

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Access by PDB/NDB ID
	4hn1
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UniProtKB/Swiss-Prot
	CHMJ_STRBI \| Q5SFD1	:	4hmz 4hn0

4hmz	CRYSTAL STRUCTURE OF CHMJ, A 3'-MONOEPIMERASE FROM STREPTOMYCES BIKINIENSIS IN COMPLEX WITH DTDP-QUINOVOSE
4hn0	CRYSTAL STRUCTURE OF CHMJ, A 3'-MONOEPIMERASE APOENZYME FROM STREPTOMYCES BIKINIENSIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Gene Ontology (4, 4)

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